Skip to content
Snippets Groups Projects
Commit 22db3a03 authored by Gareth Tribello's avatar Gareth Tribello
Browse files

Changed regtest for PCA so as to test outputting molinfo stuff in pdb

parent a7637c36
No related branches found
No related tags found
No related merge requests found
Hide whitespace changes
Inline Side-by-side
regtest/dimred/rt-pca/pca-comp.pdb.reference
+ 66
− 66
View file @ 22db3a03
REMARK TYPE=OPTIMAL REMARK TYPE=OPTIMAL
ATOM 1 X RES 0 -3.002 -0.303 1.042 1.00 1.00 ATOM 1 CL ALA 1 -3.002 -0.303 1.042 1.00 1.00
ATOM 2 X RES 1 -3.375 -0.131 1.046 1.00 1.00 ATOM 2 HL1 ALA 1 -3.375 -0.131 1.046 1.00 1.00
ATOM 3 X RES 2 -3.376 -0.402 1.084 1.00 1.00 ATOM 3 HL2 ALA 1 -3.376 -0.402 1.084 1.00 1.00
ATOM 4 X RES 3 -3.326 -0.239 1.294 1.00 1.00 ATOM 4 HL3 ALA 1 -3.326 -0.239 1.294 1.00 1.00
ATOM 5 X RES 4 -1.625 -0.479 0.681 1.00 1.00 ATOM 5 CLP ALA 1 -1.625 -0.479 0.681 1.00 1.00
ATOM 6 X RES 5 -1.001 -0.681 1.355 1.00 1.00 ATOM 6 OL ALA 1 -1.001 -0.681 1.355 1.00 1.00
ATOM 7 X RES 6 -1.117 -0.412 -0.407 1.00 1.00 ATOM 7 NL ALA 1 -1.117 -0.412 -0.407 1.00 1.00
ATOM 8 X RES 7 -1.688 -0.225 -0.895 1.00 1.00 ATOM 8 HL ALA 1 -1.688 -0.225 -0.895 1.00 1.00
ATOM 9 X RES 8 0.167 -0.648 -0.993 1.00 1.00 ATOM 9 CA ALA 1 0.167 -0.648 -0.993 1.00 1.00
ATOM 10 X RES 9 0.264 -1.677 -1.119 1.00 1.00 ATOM 10 HA ALA 1 0.264 -1.677 -1.119 1.00 1.00
ATOM 11 X RES 10 0.199 -0.014 -2.349 1.00 1.00 ATOM 11 CB ALA 1 0.199 -0.014 -2.349 1.00 1.00
ATOM 12 X RES 11 0.278 0.101 -2.643 1.00 1.00 ATOM 12 HB1 ALA 1 0.278 0.101 -2.643 1.00 1.00
ATOM 13 X RES 12 0.168 0.098 -2.737 1.00 1.00 ATOM 13 HB2 ALA 1 0.168 0.098 -2.737 1.00 1.00
ATOM 14 X RES 13 0.174 0.229 -2.704 1.00 1.00 ATOM 14 HB3 ALA 1 0.174 0.229 -2.704 1.00 1.00
ATOM 15 X RES 14 1.392 -0.272 -0.203 1.00 1.00 ATOM 15 CRP ALA 1 1.392 -0.272 -0.203 1.00 1.00
ATOM 16 X RES 15 2.259 -0.716 -0.363 1.00 1.00 ATOM 16 OR ALA 1 2.259 -0.716 -0.363 1.00 1.00
ATOM 17 X RES 16 1.500 0.569 0.661 1.00 1.00 ATOM 17 NR ALA 1 1.500 0.569 0.661 1.00 1.00
ATOM 18 X RES 17 0.762 0.889 0.785 1.00 1.00 ATOM 18 HR ALA 1 0.762 0.889 0.785 1.00 1.00
ATOM 19 X RES 18 2.611 0.994 1.452 1.00 1.00 ATOM 19 CR ALA 1 2.611 0.994 1.452 1.00 1.00
ATOM 20 X RES 19 2.964 1.128 1.574 1.00 1.00 ATOM 20 HR1 ALA 1 2.964 1.128 1.574 1.00 1.00
ATOM 21 X RES 20 2.843 1.185 1.726 1.00 1.00 ATOM 21 HR2 ALA 1 2.843 1.185 1.726 1.00 1.00
ATOM 22 X RES 21 2.928 1.006 1.713 1.00 1.00 ATOM 22 HR3 ALA 1 2.928 1.006 1.713 1.00 1.00
END END
REMARK TYPE=DIRECTION REMARK TYPE=DIRECTION
ATOM 1 X RES 0 0.354 0.171 0.229 1.00 1.00 ATOM 1 CL ALA 1 0.354 0.171 0.229 1.00 1.00
ATOM 2 X RES 1 0.585 0.567 0.558 1.00 1.00 ATOM 2 HL1 ALA 1 0.585 0.567 0.558 1.00 1.00
ATOM 3 X RES 2 0.205 0.793 0.037 1.00 1.00 ATOM 3 HL2 ALA 1 0.205 0.793 0.037 1.00 1.00
ATOM 4 X RES 3 0.320 0.180 0.111 1.00 1.00 ATOM 4 HL3 ALA 1 0.320 0.180 0.111 1.00 1.00
ATOM 5 X RES 4 0.255 -1.235 0.169 1.00 1.00 ATOM 5 CLP ALA 1 0.255 -1.235 0.169 1.00 1.00
ATOM 6 X RES 5 0.252 -4.529 0.304 1.00 1.00 ATOM 6 OL ALA 1 0.252 -4.529 0.304 1.00 1.00
ATOM 7 X RES 6 0.252 1.215 -0.073 1.00 1.00 ATOM 7 NL ALA 1 0.252 1.215 -0.073 1.00 1.00
ATOM 8 X RES 7 0.435 3.800 -0.249 1.00 1.00 ATOM 8 HL ALA 1 0.435 3.800 -0.249 1.00 1.00
ATOM 9 X RES 8 0.107 0.313 -0.066 1.00 1.00 ATOM 9 CA ALA 1 0.107 0.313 -0.066 1.00 1.00
ATOM 10 X RES 9 0.093 0.161 1.087 1.00 1.00 ATOM 10 HA ALA 1 0.093 0.161 1.087 1.00 1.00
ATOM 11 X RES 10 -0.089 -1.113 -0.746 1.00 1.00 ATOM 11 CB ALA 1 -0.089 -1.113 -0.746 1.00 1.00
ATOM 12 X RES 11 0.480 -3.066 -1.776 1.00 1.00 ATOM 12 HB1 ALA 1 0.480 -3.066 -1.776 1.00 1.00
ATOM 13 X RES 12 -2.025 -1.152 -0.684 1.00 1.00 ATOM 13 HB2 ALA 1 -2.025 -1.152 -0.684 1.00 1.00
ATOM 14 X RES 13 1.185 -0.261 -0.272 1.00 1.00 ATOM 14 HB3 ALA 1 1.185 -0.261 -0.272 1.00 1.00
ATOM 15 X RES 14 0.099 1.372 -0.666 1.00 1.00 ATOM 15 CRP ALA 1 0.099 1.372 -0.666 1.00 1.00
ATOM 16 X RES 15 0.492 3.830 -2.307 1.00 1.00 ATOM 16 OR ALA 1 0.492 3.830 -2.307 1.00 1.00
ATOM 17 X RES 16 -0.394 -0.438 0.775 1.00 1.00 ATOM 17 NR ALA 1 -0.394 -0.438 0.775 1.00 1.00
ATOM 18 X RES 17 -0.608 -2.369 1.984 1.00 1.00 ATOM 18 HR ALA 1 -0.608 -2.369 1.984 1.00 1.00
ATOM 19 X RES 18 -0.479 0.302 0.455 1.00 1.00 ATOM 19 CR ALA 1 -0.479 0.302 0.455 1.00 1.00
ATOM 20 X RES 19 -0.662 0.700 0.477 1.00 1.00 ATOM 20 HR1 ALA 1 -0.662 0.700 0.477 1.00 1.00
ATOM 21 X RES 20 -0.547 0.209 0.491 1.00 1.00 ATOM 21 HR2 ALA 1 -0.547 0.209 0.491 1.00 1.00
ATOM 22 X RES 21 -0.309 0.548 0.162 1.00 1.00 ATOM 22 HR3 ALA 1 -0.309 0.548 0.162 1.00 1.00
END END
REMARK TYPE=DIRECTION REMARK TYPE=DIRECTION
ATOM 1 X RES 0 0.040 -0.180 0.140 1.00 1.00 ATOM 1 CL ALA 1 0.040 -0.180 0.140 1.00 1.00
ATOM 2 X RES 1 0.469 -1.519 2.216 1.00 1.00 ATOM 2 HL1 ALA 1 0.469 -1.519 2.216 1.00 1.00
ATOM 3 X RES 2 0.337 2.166 0.164 1.00 1.00 ATOM 3 HL2 ALA 1 0.337 2.166 0.164 1.00 1.00
ATOM 4 X RES 3 -0.723 -1.344 -1.892 1.00 1.00 ATOM 4 HL3 ALA 1 -0.723 -1.344 -1.892 1.00 1.00
ATOM 5 X RES 4 0.011 -0.017 0.057 1.00 1.00 ATOM 5 CLP ALA 1 0.011 -0.017 0.057 1.00 1.00
ATOM 6 X RES 5 0.044 0.234 -0.008 1.00 1.00 ATOM 6 OL ALA 1 0.044 0.234 -0.008 1.00 1.00
ATOM 7 X RES 6 -0.006 -0.149 0.077 1.00 1.00 ATOM 7 NL ALA 1 -0.006 -0.149 0.077 1.00 1.00
ATOM 8 X RES 7 -0.009 -0.335 0.106 1.00 1.00 ATOM 8 HL ALA 1 -0.009 -0.335 0.106 1.00 1.00
ATOM 9 X RES 8 -0.007 -0.045 0.002 1.00 1.00 ATOM 9 CA ALA 1 -0.007 -0.045 0.002 1.00 1.00
ATOM 10 X RES 9 0.008 -0.058 -0.089 1.00 1.00 ATOM 10 HA ALA 1 0.008 -0.058 -0.089 1.00 1.00
ATOM 11 X RES 10 -0.099 0.067 0.048 1.00 1.00 ATOM 11 CB ALA 1 -0.099 0.067 0.048 1.00 1.00
ATOM 12 X RES 11 2.890 -0.426 -0.116 1.00 1.00 ATOM 12 HB1 ALA 1 2.890 -0.426 -0.116 1.00 1.00
ATOM 13 X RES 12 -2.066 -1.963 -0.898 1.00 1.00 ATOM 13 HB2 ALA 1 -2.066 -1.963 -0.898 1.00 1.00
ATOM 14 X RES 13 -1.117 2.728 1.157 1.00 1.00 ATOM 14 HB3 ALA 1 -1.117 2.728 1.157 1.00 1.00
ATOM 15 X RES 14 0.018 -0.063 0.016 1.00 1.00 ATOM 15 CRP ALA 1 0.018 -0.063 0.016 1.00 1.00
ATOM 16 X RES 15 0.077 -0.275 0.135 1.00 1.00 ATOM 16 OR ALA 1 0.077 -0.275 0.135 1.00 1.00
ATOM 17 X RES 16 -0.013 0.160 -0.129 1.00 1.00 ATOM 17 NR ALA 1 -0.013 0.160 -0.129 1.00 1.00
ATOM 18 X RES 17 -0.037 0.355 -0.233 1.00 1.00 ATOM 18 HR ALA 1 -0.037 0.355 -0.233 1.00 1.00
ATOM 19 X RES 18 0.046 0.169 -0.200 1.00 1.00 ATOM 19 CR ALA 1 0.046 0.169 -0.200 1.00 1.00
ATOM 20 X RES 19 2.278 -3.179 -1.474 1.00 1.00 ATOM 20 HR1 ALA 1 2.278 -3.179 -1.474 1.00 1.00
ATOM 21 X RES 20 0.240 3.803 -2.326 1.00 1.00 ATOM 21 HR2 ALA 1 0.240 3.803 -2.326 1.00 1.00
ATOM 22 X RES 21 -2.383 -0.130 3.246 1.00 1.00 ATOM 22 HR3 ALA 1 -2.383 -0.130 3.246 1.00 1.00
END END
regtest/dimred/rt-pca/plumed.dat
+ 1
− 0
View file @ 22db3a03
MOLINFO STRUCTURE=diala-template.pdb
ff: COLLECT_FRAMES ATOMS=1-22 STRIDE=1 ff: COLLECT_FRAMES ATOMS=1-22 STRIDE=1
pca: PCA USE_OUTPUT_DATA_FROM=ff NLOW_DIM=2 METRIC=OPTIMAL pca: PCA USE_OUTPUT_DATA_FROM=ff NLOW_DIM=2 METRIC=OPTIMAL
OUTPUT_PCA_PROJECTION USE_OUTPUT_DATA_FROM=pca FILE=pca-comp.pdb OUTPUT_PCA_PROJECTION USE_OUTPUT_DATA_FROM=pca FILE=pca-comp.pdb
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment